[gmx-users] Dubious results with NPT
sujithkakkat .
sujithks58 at gmail.com
Fri Mar 14 09:02:05 CET 2014
Hello,
This time I tried sesiisotropic scaling with Berendsen Barostat. The
compressibility was set to zero in Z-direction allowing scaling only in X
and Y. The NPT simulation was run for 10ns.
The result did not look good and the average pressure was ~36 bar
(reference pressure is 1 bar).
Even more confusing was the graphs of various properties against time.
Pressure vs time shows a sudden decrease in fluctuations at about 5ns and
thereafter . The pressure fluctuations lowered to around ~170bar from ~650
bar.
A dramatic change was observed in many properties at around this time. For
eg, the short range LJ interaction was found to decrease sharply at ~5ns.
Also, total energy, Kinetic, Potential energies and the temperature showed
a rapid drop in the magnitude of their fluctuations from the same time.
Nothing notable was observed in the system trajectory at around this
time. I am totally confused, and I feel that I made some very bad choice
again the MDP file given below.
Please let me know what you think. Suggest something on this issue which I
should read about.
; 7.3.3 Run Control
integrator = md
tinit = 0
dt = 0.001
nsteps = 10000000
comm_mode = Linear
nstcomm = 1
comm_grps = CHX SOL
; 7.3.8 Output Control
nstxout = 25000
nstvout = 25000
nstfout = 25000
nstlog = 100
nstenergy = 100
nstxtcout = 100
xtc_precision = 1000
xtc_grps = System
energygrps = System
; 7.3.9 Neighbor Searching
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 0.9
; 7.3.10 Electrostatics
coulombtype = PME
rcoulomb = 0.9
; 7.3.11 VdW
vdwtype = cut-off
rvdw = 1.4
DispCorr = EnerPres
; 7.3.13 Ewald
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
; 7.3.14 Temperature Coupling
tcoupl = nose-hoover
tc_grps = CHX SOL
tau_t = 0.5 0.5
ref_t = 298 298
; 7.3.15 Pressure Coupling
pcoupl = berendsen
pcoupltype = semiisotropic
tau_p = 2.0
compressibility = 4.5e-5 0.0
ref_p = 1.0 1.0
; 7.3.17 Velocity Generation
gen_vel = no
gen_temp = 298
gen_seed = -1
; 7.3.18 Bonds
constraints = none
constraint_algorithm = LINCS
continuation = no
lincs_order = 4
lincs_iter = 1
lincs_warnangle = 30
Regards,
Sujith.
On Wed, Mar 12, 2014 at 5:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 3/12/14, 7:51 AM, sujithkakkat . wrote:
>
>> Hello,
>>
>> After a while I got back to the problem posted here. This issue was the
>> large value for average pressure(~25 bar against the reference pressure
>> of
>> 1 bar) in NPT simulations with parrinello rahman barostat. The system
>> studied is cyclohexane-water system with an interface.
>> The forcefield is Gromos96. Gromacs 4.6.5 version is used.
>>
>> I recollect a post from Michael Shirts which says that with systems that
>> are heterogeneous in direction (not uniform in x y and z), any errors in
>> the pressure may be magnified. Is this what is happening in my case?
>>
>> Based on your suggestions , I tried the following to analyze/solve the
>> problem, and till now the results have not improved a bit.
>>
>> (i) The system was simplified. Each phases was simulated separately. The
>> results were good, with proper values of average pressure after NPT
>> simulation for both independent water and cyclohexane systems. However,
>> when doing the same with similar parameters on the water-cyclohexane
>> combined system with parrinello-rahman barostat , still gives very high
>> average pressure (even after 10ns )
>>
>> (ii) Changing the tau_p values did not help either. (I tried 1ps, 2ps,
>> and 4ps)
>>
>> My question is whether, I can try the semiisotropic scaling? The manual
>> says that it is useful in case of systems with interface. I am not sure,
>> since none of the replies I got suggested that option, which gives the
>> impression that it is not the best solution. But , to my limited knowledge
>> that is the only option left to be tried to solve the issue.
>>
>>
> Worth a shot. Also try changing the barostat to Berendsen to see if that
> changes anything. There are a lot of interrelated issues here, possibly a
> problem with the barostat, the tau_p value, the type of coupling, the
> combination of the integrator and barostat...you see how complicated it
> gets, and that's only some of the possible issues.
>
> -Justin
>
>
>
>> The mdp file used is,
>>
>> ; 7.3.3 Run Control
>> integrator = md
>> tinit = 0
>> dt = 0.001
>> nsteps = 10000000
>> comm_mode = Linear
>> nstcomm = 1
>> comm_grps = CHX SOL
>>
>> ; 7.3.8 Output Control
>> nstxout = 25000
>> nstvout = 25000
>> nstfout = 25000
>> nstlog = 100
>> nstenergy = 100
>> nstxtcout = 100
>> xtc_precision = 1000
>> xtc_grps = System
>> energygrps = System
>>
>> ; 7.3.9 Neighbor Searching
>> nstlist = 10
>> ns_type = grid
>> pbc = xyz
>> rlist = 0.9
>>
>> ; 7.3.10 Electrostatics
>> coulombtype = PME
>> rcoulomb = 0.9
>>
>> ; 7.3.11 VdW
>> vdwtype = cut-off
>> rvdw = 1.4
>> DispCorr = EnerPres
>>
>> ; 7.3.13 Ewald
>> fourierspacing = 0.12
>> pme_order = 4
>> ewald_rtol = 1e-5
>>
>> ; 7.3.14 Temperature Coupling
>> tcoupl = nose-hoover
>> tc_grps = CHX SOL
>> tau_t = 0.5 0.5
>> ref_t = 298 298
>>
>> ; 7.3.15 Pressure Coupling
>> pcoupl = parrinello-rahman
>> pcoupltype = isotropic
>> tau_p = 2.0
>> compressibility = 4.5e-5
>> ref_p = 1.0
>>
>>
>> ; 7.3.17 Velocity Generation
>> gen_vel = no
>> gen_temp = 298
>> gen_seed = -1
>>
>> ; 7.3.18 Bonds
>> constraints = none
>> constraint_algorithm = LINCS
>> continuation = no
>> lincs_order = 4
>> lincs_iter = 1
>> lincs_warnangle = 30
>>
>>
>>
>> Please comment.
>>
>> Sujith.
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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